def setup(self): ### Main class setup method.
'''Main class setup method.'''
try:### ~ [1] ~ Setup Program ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
self.obj['Prog'] = None
prog = self.getStrLC('Name')
if prog in mod:
i = self.obj['ProgInfo'] = mod[prog].makeInfo()
self.printLog('#PROG','%s V%s: %s' % (i.program,i.version,i.description))
progcmd = rje.getCmdList([],info=i) + self.cmd_list + ['newlog=F']
out = rje.Out(cmd_list=progcmd)
out.printIntro(i)
#self.debug(prog); self.debug(progcmd)
if self.getBool('Help'): progcmd = mod[prog].cmdHelp(i,out,['help']+progcmd)
self.printLog('#CMD','Full %s CmdList: %s' % (i.program,rje.argString(rje.tidyArgs(progcmd,nopath=self.getStrLC('Rest') and not self.dev(),purgelist=purgelist))),screen=False)
#self.debug(prog); self.debug(progcmd)
## ~ [1a] ~ Make self.obj['Prog'] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
if prog in ['seqlist','rje_seqlist']: self.obj['Prog'] = rje_seqlist.SeqList(self.log,progcmd)
elif prog in ['uniprot','rje_uniprot']: self.obj['Prog'] = rje_uniprot.UniProt(self.log,progcmd)
elif prog in ['taxonomy','rje_taxonomy']: self.obj['Prog'] = rje_taxonomy.Taxonomy(self.log,progcmd)
elif prog in ['tree','rje_tree']: self.obj['Prog'] = rje_tree.Tree(self.log,progcmd)
elif prog in ['xref','rje_xref']: self.obj['Prog'] = rje_xref.XRef(self.log,progcmd)
elif prog in ['seq','rje_seq']: self.obj['Prog'] = rje_seq.SeqList(self.log,progcmd)
elif prog in ['mitab','rje_mitab']: self.obj['Prog'] = rje_mitab.MITAB(self.log,progcmd)
elif prog in ['dbase','database']: self.obj['Prog'] = rje_dbase.DatabaseController(self.log,progcmd)
elif prog in ['pydocs']: self.obj['Prog'] = rje_pydocs.PyDoc(self.log,progcmd)
elif prog in ['ensembl','rje_ensembl']: self.obj['Prog'] = rje_ensembl.EnsEMBL(self.log,progcmd)
elif prog in ['genbank','rje_genbank']: self.obj['Prog'] = rje_genbank.GenBank(self.log,progcmd)
elif prog in ['extatic']: self.obj['Prog'] = extatic.ExTATIC(self.log,progcmd)
elif prog in ['revert']: self.obj['Prog'] = revert.REVERT(self.log,progcmd)
elif prog in ['fiesta']: self.obj['Prog'] = fiesta.FIESTA(self.log,progcmd)
elif prog in ['gablam']: self.obj['Prog'] = gablam.GABLAM(self.log,progcmd)
elif prog in ['gopher']: self.obj['Prog'] = gopher.Gopher(self.log,progcmd)
elif prog in ['haqesac']: self.obj['Prog'] = haqesac.HAQESAC(self.log,progcmd)
elif prog in ['multihaq']: self.obj['Prog'] = multihaq.MultiHAQ(self.log,progcmd)
elif prog in ['pingu']: self.obj['Prog'] = pingu.PINGU(self.log,progcmd)
elif prog in ['pacbio']: self.obj['Prog'] = rje_pacbio.PacBio(self.log,progcmd)
elif prog in ['rje_zen','zen']: self.obj['Prog'] = rje_zen.Zen(self.log,progcmd)
### ~ [2] ~ Failure to recognise program ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
if not self.obj['Prog']:
self.printLog('#ERR','Program "%s" not recognised.' % self.getStr('Name'))
if self.i() < 0: return False
if rje.yesNo('Show SeqSuite help with program options?'):
extracmd = cmdHelp(cmd_list=['help'])[1:]
if extracmd:
self.cmd_list += extracmd
self._cmdList()
if prog != self.getStrLC('Name'): return self.setup()
self.setStr({'Name':rje.choice('Give program name (Blank or CTRL+C to quit)')})
if self.getStrLC('Name'): return self.setup()
else: return False
return self.obj['Prog'] # Setup successful
except KeyboardInterrupt: return False
except SystemExit: raise
except: self.errorLog('Problem during %s setup.' % self.prog()); return False # Setup failed
def setup(self,rest=False): ### Main class setup method.
'''Main class setup method.'''
try:### ~ [1] ~ Setup Program ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
self.obj['Prog'] = None
prog = self.getStrLC('Name')
if prog in mod:
i = self.obj['ProgInfo'] = mod[prog].makeInfo()
self.printLog('#PROG','%s V%s: %s' % (i.program,i.version,i.description))
progcmd = rje.getCmdList([],info=i) + self.cmd_list + ['newlog=F']
out = rje.Out(cmd_list=progcmd)
out.printIntro(i)
if self.getBool('Help'): progcmd = mod[prog].cmdHelp(i,out,['help']+progcmd)
purgelist = seqsuite.purgelist
self.printLog('#CMD','Full %s CmdList: %s' % (i.program,rje.argString(rje.tidyArgs(progcmd,nopath=self.getStrLC('Rest') and not self.dev(),purgelist=purgelist))),screen=False)
#self.debug(prog)
## ~ [1a] ~ Make self.obj['Prog'] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
if prog in ['slimcore','rje_slimcore','core']: self.obj['Prog'] = rje_slimcore.SLiMCore(self.log,progcmd)
elif prog in ['rlc','iuscore']: self.obj['Prog'] = rje_slimcore.SLiMCore(self.log,progcmd+['prog=%s' % prog])
elif prog in ['slimlist','rje_slimlist']: self.obj['Prog'] = rje_slimlist.SLiMList(self.log,progcmd)
elif prog in ['slimfinder']: self.obj['Prog'] = slimfinder.SLiMFinder(self.log,progcmd)
elif prog in ['qslimfinder']: self.obj['Prog'] = qslimfinder.QSLiMFinder(self.log,progcmd)
elif prog in ['slimprob']: self.obj['Prog'] = slimprob.SLiMProb(self.log,progcmd)
elif prog in ['slimmaker']: self.obj['Prog'] = slimmaker.SLiMMaker(self.log,progcmd)
elif prog in ['slimfarmer','farm']: self.obj['Prog'] = slimfarmer.SLiMFarmer(self.log,progcmd)
elif prog in ['slimbench']: self.obj['Prog'] = slimbench.SLiMBench(self.log,progcmd)
elif prog in ['comparimotif']: self.obj['Prog'] = comparimotif.CompariMotif(self.log,progcmd)
elif prog in ['peptcluster']: self.obj['Prog'] = peptcluster.PeptCluster(self.log,progcmd)
elif prog in ['peptalign']: self.obj['Prog'] = peptcluster.PeptCluster(self.log,['peptalign=T']+progcmd+['peptdis=None'])
self.obj['Prog'].dict['Output']['help'] = mod[prog].__doc__
elif prog in seqsuite.mod:
seqsuiteobj = seqsuite.SeqSuite(self.log,self.cmd_list)
self.obj['Prog'] = seqsuiteobj.setup()
self.obj['ProgInfo'] = seqsuiteobj.obj['ProgInfo']
self.obj['Prog'].dict['Output']['help'] = seqsuite.mod[prog].__doc__
### ~ [2] ~ Failure to recognise program ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
if not self.obj['Prog']:
if self.getStrLC('Name') != 'help':
if not rest: self.printLog('#ERR','Program "%s" not recognised.' % self.getStr('Name'))
if self.i() < 0 or rest: return False
#!# Try SeqSuite? #!#
if self.getStrLC('Name') == 'help' or rje.yesNo('Show SLiMSuite help with program options?'):
extracmd = cmdHelp(cmd_list=['help'])[1:]
if extracmd:
self.cmd_list += extracmd
self._cmdList()
if prog != self.getStrLC('Name'): return self.setup()
self.setStr({'Name':rje.choice('Give program name (Blank or CTRL+C to quit)')})
if self.getStrLC('Name'): return self.setup()
else: return False
return self.obj['Prog'] # Setup successful
except KeyboardInterrupt: return False
except SystemExit: raise
except: self.errorLog('Problem during %s setup.' % self.prog()); return False # Setup failed
def setup(self): ### Main class setup method.
'''Main class setup method.'''
try: ### ~ [1] ~ Setup Program ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
self.obj['Prog'] = None
prog = self.getStrLC('Name')
if prog in mod:
i = self.obj['ProgInfo'] = mod[prog].makeInfo()
self.printLog(
'#PROG',
'%s V%s: %s' % (i.program, i.version, i.description))
progcmd = rje.getCmdList(
[], info=i) + self.cmd_list + ['newlog=F']
out = rje.Out(cmd_list=progcmd)
out.printIntro(i)
if self.getBool('Help'):
progcmd = mod[prog].cmdHelp(i, out, ['help'] + progcmd)
purgelist = seqsuite.purgelist
self.printLog('#CMD',
'Full %s CmdList: %s' %
(i.program,
rje.argString(
rje.tidyArgs(progcmd,
nopath=self.getStrLC('Rest')
and not self.dev(),
purgelist=purgelist))),
screen=False)
#self.debug(prog)
## ~ [1a] ~ Make self.obj['Prog'] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
if prog in ['slimcore', 'rje_slimcore']:
self.obj['Prog'] = rje_slimcore.SLiMCore(self.log, progcmd)
elif prog in ['rlc', 'disorder']:
self.obj['Prog'] = rje_slimcore.SLiMCore(
self.log, progcmd + ['prog=%s' % prog])
elif prog in ['slimlist', 'rje_slimlist']:
self.obj['Prog'] = rje_slimlist.SLiMList(self.log, progcmd)
elif prog in ['slimfinder']:
self.obj['Prog'] = slimfinder.SLiMFinder(self.log, progcmd)
elif prog in ['qslimfinder']:
self.obj['Prog'] = qslimfinder.QSLiMFinder(
self.log, progcmd)
elif prog in ['slimprob']:
self.obj['Prog'] = slimprob.SLiMProb(self.log, progcmd)
elif prog in ['slimmaker']:
self.obj['Prog'] = slimmaker.SLiMMaker(self.log, progcmd)
elif prog in ['slimfarmer', 'farm']:
self.obj['Prog'] = slimfarmer.SLiMFarmer(self.log, progcmd)
elif prog in ['slimbench']:
self.obj['Prog'] = slimbench.SLiMBench(self.log, progcmd)
elif prog in ['comparimotif']:
self.obj['Prog'] = comparimotif.CompariMotif(
self.log, progcmd)
elif prog in ['peptcluster']:
self.obj['Prog'] = peptcluster.PeptCluster(
self.log, progcmd)
elif prog in ['peptalign']:
self.obj['Prog'] = peptcluster.PeptCluster(
self.log, ['peptalign=T'] + progcmd)
self.obj['Prog'].dict['Output']['help'] = mod[prog].__doc__
elif prog in seqsuite.mod:
seqsuiteobj = seqsuite.SeqSuite(self.log, self.cmd_list)
self.obj['Prog'] = seqsuiteobj.setup()
self.obj['ProgInfo'] = seqsuiteobj.obj['ProgInfo']
self.obj['Prog'].dict['Output']['help'] = seqsuite.mod[
prog].__doc__
### ~ [2] ~ Failure to recognise program ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
if not self.obj['Prog']:
self.printLog(
'#ERR',
'Program "%s" not recognised.' % self.getStr('Name'))
if self.i() < 0: return False
#!# Try SeqSuite? #!#
if rje.yesNo('Show SLiMSuite help with program options?'):
extracmd = cmdHelp(cmd_list=['help'])[1:]
if extracmd:
self.cmd_list += extracmd
self._cmdList()
if prog != self.getStrLC('Name'): return self.setup()
self.setStr({
'Name':
rje.choice('Give program name (Blank or CTRL+C to quit)')
})
if self.getStrLC('Name'): return self.setup()
else: return False
return self.obj['Prog'] # Setup successful
except KeyboardInterrupt:
return False
except SystemExit:
raise
except:
self.errorLog('Problem during %s setup.' % self.prog())
return False # Setup failed
def gff3(self,locdb,sumdb,exmodel,filename=''): ### Converts local and summary tables into GFF table.
'''
Converts local and summary tables into GFF table.
:param locdb: Local hits database Table
:param sumdb: Hit summary database Table
:param exmodel: Exonerate model
:param filename: Save to filename, if given.
:return: GFF database Table
'''
try:### ~ [0] Setup ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
if not exmodel: exmodel = 'dna2dna'
lochits = {} # Dictionary of {hitsumkey:[local entries]}
for hkey in sumdb.dataKeys(): lochits[hkey] = []
for lkey in locdb.dataKeys():
entry = locdb.data(lkey)
hkey = (entry['Qry'],entry['Rank'],entry['Hit'])
if hkey in lochits: lochits[hkey].append(entry)
else: self.warnLog('Local hit (%s) without summary (%s)' % (lkey,hkey))
gffdb = self.db().copyTable(locdb,'%sgff' % locdb.name()[:3])
gffdb.addField('type',evalue='similarity') #!# Add cds and gene types
gffdb.addField('attributes',evalue='') #!# Add cds and gene types
e2gfields = [('Hit','seqid'), ('HitStart','start'), ('HitEnd','end'), ('Phase','phase'), ('Score','score'), ('HitStrand','strand')]
gfields = string.split('seqid source type start end score strand phase attributes')
# ID is unique
# Name is not unique
# Parent links exons or cds to gene
geneid = {}
for hkey in sumdb.dataKeys():
entry = sumdb.data(hkey)
entry['Phase'] = '.'
entry['AlnID'] = entry['Rank']
geneid[hkey] = '%s-%d' % (entry['Qry'],entry['Rank'])
entry['attributes'] = 'ID=%s;Name=%s;' % (geneid[hkey],geneid[hkey])
if 'QryDesc' in sumdb.fields(): entry['attributes'] += 'Note=Similar to %s;' % (entry['QryDesc'])
if exmodel in ['est2genome','protein2genome']: entry['type'] = 'gene'
else: entry['type'] = 'similarity'
gffdb.addEntry(entry)
for lkey in locdb.dataKeys():
entry = gffdb.data(lkey)
hkey = (entry['Qry'],entry['Rank'],entry['Hit'])
if exmodel in ['est2genome','protein2genome']: entry['type'] = 'CDS'
entry['attributes'] = 'ID=%s:%s;Parent=%s;Name=%s-%s;' % (geneid[hkey],entry['type'],geneid[hkey],geneid[hkey],entry['AlnID'])
gffdb.addField('source',evalue='rje_apollo:exonerate:%s' % exmodel)
qrytype = 'Qry'
for entry in gffdb.entries():
if entry['HitStart'] > entry['HitEnd']:
[entry['HitStart'], entry['HitEnd']] = [entry['HitEnd'],entry['HitStart']]
entry['attributes'] += 'qstart=%s;' % min(entry['%sStart' % qrytype],entry['%sEnd' % qrytype])
entry['attributes'] += 'qend=%s;' % max(entry['%sStart' % qrytype],entry['%sEnd' % qrytype])
if 'QryLen' in entry and entry['QryLen']:
field = 'QryLen'
entry['attributes'] += 'qrylen=%s;' % (entry[field])
entry['attributes'] += 'identity=%s;' % (entry['Identity'])
entry['attributes'] += 'score=%s;' % (entry['Score'])
entry['attributes'] = entry['attributes'][:-1]
for (ef,gf) in e2gfields:
if ef in gffdb.fields():
gffdb.renameField(ef,gf)
else: gffdb.addField(gf,evalue='.')
gffdb.newKey(['seqid','start','AlnID','end','type','source','attributes'])
gffdb.keepFields(gfields+['AlnID'])
### ~ [2] Output GFF File ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
if filename:
gcomments = ['##gff-version 3','#Generated by %s' % self.log.runDetails()]
if not self.getStrLC('Rest'): gcomments.append('#Full Command List: %s' % rje.argString(rje.tidyArgs(self.log.cmd_list)))
gffdb.saveToFile(filename,delimit='\t',backup=True,append=False,savefields=gfields,log=True,headers=False,comments=gcomments)
return gffdb
except: self.errorLog('%s.gff3 error' % self.prog()); raise
def setup(self): ### Main class setup method.
'''Main class setup method.'''
try: ### ~ [1] ~ Setup Program ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
self.obj['Prog'] = None
prog = self.getStrLC('Name')
if prog in mod:
i = self.obj['ProgInfo'] = mod[prog].makeInfo()
self.printLog(
'#PROG',
'%s V%s: %s' % (i.program, i.version, i.description))
progcmd = rje.getCmdList(
[], info=i) + self.cmd_list + ['newlog=F']
out = rje.Out(cmd_list=progcmd)
out.printIntro(i)
#self.debug(prog); self.debug(progcmd)
if self.getBool('Help'):
progcmd = mod[prog].cmdHelp(i, out, ['help'] + progcmd)
self.printLog('#CMD',
'Full %s CmdList: %s' %
(i.program,
rje.argString(
rje.tidyArgs(progcmd,
nopath=self.getStrLC('Rest')
and not self.dev(),
purgelist=purgelist))),
screen=False)
#self.debug(prog); self.debug(progcmd)
## ~ [1a] ~ Make self.obj['Prog'] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
if prog in ['seqlist', 'rje_seqlist']:
self.obj['Prog'] = rje_seqlist.SeqList(self.log, progcmd)
elif prog in ['uniprot', 'rje_uniprot']:
self.obj['Prog'] = rje_uniprot.UniProt(self.log, progcmd)
elif prog in ['taxonomy', 'rje_taxonomy']:
self.obj['Prog'] = rje_taxonomy.Taxonomy(self.log, progcmd)
elif prog in ['tree', 'rje_tree']:
self.obj['Prog'] = rje_tree.Tree(self.log, progcmd)
elif prog in ['xref', 'rje_xref']:
self.obj['Prog'] = rje_xref.XRef(self.log, progcmd)
elif prog in ['seq', 'rje_seq']:
self.obj['Prog'] = rje_seq.SeqList(self.log, progcmd)
elif prog in ['mitab', 'rje_mitab']:
self.obj['Prog'] = rje_mitab.MITAB(self.log, progcmd)
elif prog in ['dbase', 'database']:
self.obj['Prog'] = rje_dbase.DatabaseController(
self.log, progcmd)
elif prog in ['pydocs']:
self.obj['Prog'] = rje_pydocs.PyDoc(self.log, progcmd)
elif prog in ['ensembl', 'rje_ensembl']:
self.obj['Prog'] = rje_ensembl.EnsEMBL(self.log, progcmd)
elif prog in ['genbank', 'rje_genbank']:
self.obj['Prog'] = rje_genbank.GenBank(self.log, progcmd)
elif prog in ['extatic']:
self.obj['Prog'] = extatic.ExTATIC(self.log, progcmd)
elif prog in ['revert']:
self.obj['Prog'] = revert.REVERT(self.log, progcmd)
elif prog in ['fiesta']:
self.obj['Prog'] = fiesta.FIESTA(self.log, progcmd)
elif prog in ['gablam']:
self.obj['Prog'] = gablam.GABLAM(self.log, progcmd)
elif prog in ['gopher']:
self.obj['Prog'] = gopher.Gopher(self.log, progcmd)
elif prog in ['haqesac']:
self.obj['Prog'] = haqesac.HAQESAC(self.log, progcmd)
elif prog in ['multihaq']:
self.obj['Prog'] = multihaq.MultiHAQ(self.log, progcmd)
elif prog in ['pingu']:
self.obj['Prog'] = pingu.PINGU(self.log, progcmd)
elif prog in ['pacbio']:
self.obj['Prog'] = rje_pacbio.PacBio(self.log, progcmd)
elif prog in ['rje_zen', 'zen']:
self.obj['Prog'] = rje_zen.Zen(self.log, progcmd)
### ~ [2] ~ Failure to recognise program ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
if not self.obj['Prog']:
self.printLog(
'#ERR',
'Program "%s" not recognised.' % self.getStr('Name'))
if self.i() < 0: return False
if rje.yesNo('Show SeqSuite help with program options?'):
extracmd = cmdHelp(cmd_list=['help'])[1:]
if extracmd:
self.cmd_list += extracmd
self._cmdList()
if prog != self.getStrLC('Name'): return self.setup()
self.setStr({
'Name':
rje.choice('Give program name (Blank or CTRL+C to quit)')
})
if self.getStrLC('Name'): return self.setup()
else: return False
return self.obj['Prog'] # Setup successful
except KeyboardInterrupt:
return False
except SystemExit:
raise
except:
self.errorLog('Problem during %s setup.' % self.prog())
return False # Setup failed